The Sequence Read Archive (SRA) is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental studies. The SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. The SRA stores sequencing data in a hierarchical structure. There are four levels to this hierarchy, each of which represents a particular aspect of the data:
This hierarchy is useful because it explicitly models the relationship between data files. For example, all those generated from a single sample will have the same SRS accession number. The SRA Toolkit from NCBI is a collection of tools and libraries for downloading data from the SRA using accession numbers.
Entrez is NCBI’s primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. Entrez Direct (EDirect) provides access to the NCBI’s suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a Unix terminal window. Search terms are entered as command line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats.
In this tutorial we are going to learn how to use the SRA Toolkit and EDirect to query and download public sequencing data. The first thing to do is create a directory to store all the tutorial data. It is good practice to create a new directory for each project you work on, this ensures files do not get mixed up and all the results are self-contained. Additionally we will create an installation directory where all of the conda environments we are going to use are stored.
Create a ‘tutorial’ directory to store output files:
mkdir tutorial
The software we are going to use in this tutorial can be installed using the conda package manager. Please refer to the previous conda workshop for details on installing software and creating conda environments. The first software package we need to install is the SRA Toolkit. This allows you to download sequencing data from the SRA database on the command line.
Create a new environment with the SRA Toolkit installed:
conda create --yes --name sra-tools sra-tools=2.11.0=pl5262h37d2149_1 # only this version works currently (21/09/2022)
## Collecting package metadata (current_repodata.json): ...working... done
## Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
## Collecting package metadata (repodata.json): ...working... done
## Solving environment: ...working... done
##
## ## Package Plan ##
##
## environment location: /opt/miniconda3/envs/sra-tools
##
## added / updated specs:
## - sra-tools==2.11.0=pl5262h37d2149_1
##
##
## The following NEW packages will be INSTALLED:
##
## c-ares conda-forge/osx-64::c-ares-1.18.1-h0d85af4_0
## ca-certificates conda-forge/osx-64::ca-certificates-2022.9.14-h033912b_0
## curl conda-forge/osx-64::curl-7.83.1-h23f1065_0
## hdf5 conda-forge/osx-64::hdf5-1.10.6-nompi_haae91d6_101
## icu conda-forge/osx-64::icu-70.1-h96cf925_0
## krb5 conda-forge/osx-64::krb5-1.19.3-hb98e516_0
## libcurl conda-forge/osx-64::libcurl-7.83.1-h23f1065_0
## libcxx conda-forge/osx-64::libcxx-14.0.6-hccf4f1f_0
## libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
## libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
## libgfortran conda-forge/osx-64::libgfortran-4.0.0-7_5_0_h1a10cd1_23
## libgfortran4 conda-forge/osx-64::libgfortran4-7.5.0-h1a10cd1_23
## libiconv conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
## libnghttp2 conda-forge/osx-64::libnghttp2-1.47.0-h5aae05b_1
## libssh2 conda-forge/osx-64::libssh2-1.10.0-h47af595_3
## libxml2 conda-forge/osx-64::libxml2-2.9.14-hea49891_4
## libzlib conda-forge/osx-64::libzlib-1.2.12-hfd90126_3
## llvm-openmp conda-forge/osx-64::llvm-openmp-14.0.4-ha654fa7_0
## ncbi-ngs-sdk bioconda/osx-64::ncbi-ngs-sdk-2.11.2-h247ad82_0
## ncurses conda-forge/osx-64::ncurses-6.3-h96cf925_1
## openssl conda-forge/osx-64::openssl-3.0.5-hfd90126_2
## ossuuid conda-forge/osx-64::ossuuid-1.6.2-h0a44026_1000
## perl conda-forge/osx-64::perl-5.26.2-hbcb3906_1008
## perl-uri bioconda/osx-64::perl-uri-1.71-pl526_3
## perl-xml-libxml bioconda/osx-64::perl-xml-libxml-2.0132-pl526h08abf6f_1
## perl-xml-namespac~ bioconda/osx-64::perl-xml-namespacesupport-1.11-pl526_1
## perl-xml-sax bioconda/osx-64::perl-xml-sax-0.99-pl526_1
## perl-xml-sax-base bioconda/osx-64::perl-xml-sax-base-1.09-pl526_0
## sra-tools bioconda/osx-64::sra-tools-2.11.0-pl5262h37d2149_1
## xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
## zlib conda-forge/osx-64::zlib-1.2.12-hfd90126_3
##
##
## Preparing transaction: ...working... done
## Verifying transaction: ...working... done
## Executing transaction: ...working... done
## #
## # To activate this environment, use
## #
## # $ conda activate sra-tools
## #
## # To deactivate an active environment, use
## #
## # $ conda deactivate
##
## Retrieving notices: ...working... done
Activate the new environment to use it:
conda activate sra-tools
Test that the fastq-dump command is available:
which fastq-dump
## /opt/miniconda3/envs/sra-tools/bin/fastq-dump
The second software package we need to install is the EDirect package. This allows you to search all of the NCBI databases using a text query. We are going to use it to search for public sequencing data and download the metadata associated with the sequencing libraries.
Create a new environment with EDirect installed:
conda create --yes --name entrez-direct entrez-direct
## Collecting package metadata (current_repodata.json): ...working... done
## Solving environment: ...working... done
##
## ## Package Plan ##
##
## environment location: /opt/miniconda3/envs/entrez-direct
##
## added / updated specs:
## - entrez-direct
##
##
## The following NEW packages will be INSTALLED:
##
## ca-certificates conda-forge/osx-64::ca-certificates-2022.9.14-h033912b_0
## entrez-direct bioconda/osx-64::entrez-direct-16.2-h193322a_1
## gettext conda-forge/osx-64::gettext-0.19.8.1-hd1a6beb_1008
## libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
## libiconv conda-forge/osx-64::libiconv-1.16-haf1e3a3_0
## libidn2 conda-forge/osx-64::libidn2-2.3.3-hac89ed1_0
## libunistring conda-forge/osx-64::libunistring-0.9.10-h0d85af4_0
## libzlib conda-forge/osx-64::libzlib-1.2.12-hfd90126_3
## openssl conda-forge/osx-64::openssl-3.0.5-hfd90126_2
## wget conda-forge/osx-64::wget-1.20.3-hd3787cc_1
## zlib conda-forge/osx-64::zlib-1.2.12-hfd90126_3
##
##
## Preparing transaction: ...working... done
## Verifying transaction: ...working... done
## Executing transaction: ...working... done
## #
## # To activate this environment, use
## #
## # $ conda activate entrez-direct
## #
## # To deactivate an active environment, use
## #
## # $ conda deactivate
##
## Retrieving notices: ...working... done
Activate the new environment to use it:
conda activate entrez-direct
Test that the esearch command is available:
which esearch
## /opt/miniconda3/envs/entrez-direct/bin/esearch
Prefetch is a command that is part of the SRA toolkit. This program downloads runs (sequence files in the compressed SRA format) and all additional data necessary to convert the run from the SRA format to a more commonly used format like FASTA or FASTQ files. Prefetch can also be used to correct and finish an incomplete run download. This is really helpful when you have an unstable connection as it prevents you from needing to re-download the same data repeatedly.
For this example we are going to download the run with accession SRR4413906 from the SRA database. Below is the SRA webpage listing all of the run information:
The SRA webpage provides some useful information about the sequencing run:
To fetch the sequencing data, we will use the prefetch command from the EDirect software package. This command has a lot of different parameters and we advise you to look through these before continuing.
Activate the sra-tools environment:
conda activate sra-tools
Print the help information for the prefetch command:
prefetch -h
##
## Usage: prefetch [ options ] [ accessions(s)... ]
##
## Parameters:
##
## accessions(s) list of accessions to process
##
##
## Options:
##
## -T|--type <file-type> Specify file type to download. Default: sra
## -N|--min-size <size> Minimum file size to download in KB
## (inclusive).
## -X|--max-size <size> Maximum file size to download in KB
## (exclusive). Default: 20G
## -f|--force <no|yes|all|ALL> Force object download - one of: no, yes,
## all, ALL. no [default]: skip download if
## the object if found and complete; yes:
## download it even if it is found and is
## complete; all: ignore lock files (stale
## locks or it is being downloaded by
## another process - use at your own
## risk!); ALL: ignore lock files, restart
## download from beginning
## -p|--progress Show progress
## -r|--resume <yes|no> Resume partial downloads - one of: no, yes
## [default]
## -C|--verify <yes|no> Verify after download - one of: no, yes
## [default]
## -c|--check-all Double-check all refseqs
## -o|--output-file <file> Write file to <file> when downloading
## single file
## -O|--output-directory <directory>
## Save files to <directory>/
## --ngc <path> <path> to ngc file
## --perm <path> <path> to permission file
## --location <location> location in cloud
## --cart <path> <path> to cart file
## -V|--version Display the version of the program
## -v|--verbose Increase the verbosity of the program
## status messages. Use multiple times for
## more verbosity.
## -L|--log-level <level> Logging level as number or enum string.
## One of
## (fatal|sys|int|err|warn|info|debug) or
## (0-6) Current/default is warn
## --option-file file Read more options and parameters from the
## file.
## -h|--help print this message
##
## "prefetch" version 2.11.0
Next, use the prefetch command to download the SRR4413906 run in SRA format:
# Save files to tutorial directory
prefetch --output-directory tutorial SRR4413906
##
## 2022-09-23T16:29:02 prefetch.2.11.0: 1) Downloading 'SRR4413906'...
## 2022-09-23T16:29:02 prefetch.2.11.0: Downloading via HTTPS...
## 2022-09-23T16:31:21 prefetch.2.11.0: HTTPS download succeed
## 2022-09-23T16:31:22 prefetch.2.11.0: 'SRR4413906' is valid
## 2022-09-23T16:31:22 prefetch.2.11.0: 1) 'SRR4413906' was downloaded successfully
## 2022-09-23T16:31:22 prefetch.2.11.0: 'SRR4413906' has 0 unresolved dependencies
Display the contents of the tutorial directory:
ls tutorial
## SRR4413906
The SRA file is saved in a directory named by the run accession. It is important not to move this directory as the toolkit will no longer know that we have previously downloaded the file. The toolkit keeps track of what files have been downloaded by creating an internal database of what files have been downloaded and to which location on disk.
Public sequencing data usually contains lots of runs. Multiple SRA files can be download by either providing list of run accession numbers on the command line:
# Do not run
prefetch --output-directory tutorial SRR4413817 SRR4413816 SRR4413888
Or providing a text file with a run accession number on each line:
# Do not run
prefetch --output-directory tutorial --option-file accessions.txt
Deactivate the current environment:
conda deactivate
Once the SRA file has been downloaded, we can then covert it to a more commonly used format like a FASTQ file. The fastq-dump command is used to extract FASTQ files from SRA files. Again, this command has a lot of parameters and we suggest you read through them before continuing.
Activate the sra-tools environment:
conda activate sra-tools
Print the help information for the fastq-dump command:
fastq-dump -h
##
## Usage: fastq-dump [ options ] [ accessions(s)... ]
##
## Parameters:
##
## accessions(s) list of accessions to process
##
##
## Options:
##
## -A|--accession <accession> Replaces accession derived from <path> in
## filename(s) and deflines (only for
## single table dump)
## --table <table-name> Table name within cSRA object, default is
## "SEQUENCE"
## --split-spot Split spots into individual reads
## -N|--minSpotId <rowid> Minimum spot id
## -X|--maxSpotId <rowid> Maximum spot id
## --spot-groups <[list]>[,...] Filter by SPOT_GROUP (member): name[,...]
## -W|--clip Remove adapter sequences from reads
## -M|--minReadLen <len> Filter by sequence length >= <len>
## -R|--read-filter <filter> Split into files by READ_FILTER value
## [split], optionally filter by value:
## [pass|reject|criteria|redacted]
## -E|--qual-filter Filter used in early 1000 Genomes data: no
## sequences starting or ending with >= 10N
## --qual-filter-1 Filter used in current 1000 Genomes data
## --aligned Dump only aligned sequences
## --unaligned Dump only unaligned sequences
## --aligned-region <name[:from-to]>
## Filter by position on genome. Name can
## eiter by accession.version (ex:
## NC_000001.10) or file specific name (ex:
## "chr1" or "1". "from" and "to" are
## 1-based coordinates
## --matepair_distance <from-to|unknown>
## Filter by distance between matepairs. Use
## "unknown" to find matepairs split
## between the references. Use from-to to
## limit matepair distance on the same
## reference
## --skip-technical Dump only biological reads
## -O|--outdir <path> Output directory, default is working
## directory '.'
## -Z|--stdout Output to stdout, all split data become
## joined into single stream
## --gzip Compress output using gzip: deprecated,
## not recommended
## --bzip2 Compress output using bzip2: deprecated,
## not recommended
## --split-files Write reads into separate files. Read
## number will be suffixed to the file
## name. NOTE! The `--split-3` option is
## recommended. In cases where not all
## spots have the same number of reads,
## this option will produce files that WILL
## CAUSE ERRORS in most programs which
## process split pair fastq files.
## --split-3 3-way splitting for mate-pairs. For each
## spot, if there are two biological reads
## satisfying filter conditions, the first
## is placed in the `*_1.fastq` file, and
## the second is placed in the `*_2.fastq`
## file. If there is only one biological
## read satisfying the filter conditions,
## it is placed in the `*.fastq` file.All
## other reads in the spot are ignored.
## -G|--spot-group Split into files by SPOT_GROUP (member
## name)
## -T|--group-in-dirs Split into subdirectories instead of files
## -K|--keep-empty-files Do not delete empty files
## -C|--dumpcs <cskey> Formats sequence using color space
## (default for SOLiD), "cskey" may be
## specified for translation or else
## specify "dflt" to use the default value
## -B|--dumpbase Formats sequence using base space (default
## for other than SOLiD).
## -Q|--offset <integer Offset to use for quality conversion,
## default is 33
## --fasta <line-width> FASTA only, no qualities, with can be
## "default" or "0" for no wrapping
## --suppress-qual-for-cskey suppress quality-value for cskey
## -F|--origfmt Defline contains only original sequence
## name
## -I|--readids Append read id after spot id as
## 'accession.spot.readid' on defline
## --helicos Helicos style defline
## --defline-seq <fmt> Defline format specification for sequence.
## --defline-qual <fmt> Defline format specification for quality.
## <fmt> is string of characters and/or
## variables. The variables can be one of:
## $ac - accession, $si spot id, $sn spot
## name, $sg spot group (barcode), $sl spot
## length in bases, $ri read number, $rn
## read name, $rl read length in bases.
## '[]' could be used for an optional
## output: if all vars in [] yield empty
## values whole group is not printed. Empty
## value is empty string or for numeric
## variables. Ex: @$sn[_$rn]/$ri '_$rn' is
## omitted if name is empty
## --ngc <path> <path> to ngc file
## --perm <path> <path> to permission file
## --location <location> location in cloud
## --cart <path> <path> to cart file
## --disable-multithreading disable multithreading
## -V|--version Display the version of the program
## -v|--verbose Increase the verbosity of the program
## status messages. Use multiple times for
## more verbosity.
## -L|--log-level <level> Logging level as number or enum string.
## One of
## (fatal|sys|int|err|warn|info|debug) or
## (0-6) Current/default is warn
## --option-file file Read more options and parameters from the
## file.
## -h|--help print this message
##
## "fastq-dump" version 2.11.0
There are a few important parameters to highlight here:
The --minSpotId and --maxSpotId parameters are used to download a subset of the sequencing reads. For example, setting –maxSpotId to 100 will download just the first 100 reads of a library. Setting the --minSpotId to 10 and the --maxSpotId 80 will download reads 20 to 80 of the library.
The --split-files parameter will write reads into separate files. Paired-end libraries produce two reads, one from the start and end of each DNA fragment which is sequenced. These reads need to be placed in separate files for most downstream analyses. The reads are placed in files ending with ’_1’ and ’_2’, respectively. Single-end libraries do not require you to set this parameter.
Next, convert the prefetched file from SRA format to FASTQ format:
# Convert first 100 paired-end reads
fastq-dump --maxSpotId 100 --outdir tutorial/SRR4413906 --split-files tutorial/SRR4413906/SRR4413906.sra
## Read 100 spots for tutorial/SRR4413906/SRR4413906.sra
## Written 100 spots for tutorial/SRR4413906/SRR4413906.sra
Display the contents of the output directory:
ls tutorial/SRR4413906
## SRR4413906.sra
## SRR4413906_1.fastq
## SRR4413906_2.fastq
As expected, two FASTQ files are extracted from the SRA file because the sequencing was paired-end. Each file should have the same number of reads, one from each end of the sequenced DNA fragment.
Deactivate the current environment:
conda deactivate
When handling lots of sequencing data, it is often easier to programmatically retrieve all of the associated metadata. Entrez Direct (EDirect) can be used to access this and other information from the NCBI databases. In particular, the efetch command can return formatted data records for a list of input accession numbers. As usual, this command has a lot of parameters and we suggest you read through them before continuing.
Activate the entrez-direct environment:
conda activate entrez-direct
Print the help information for the efetch command:
efetch -h
## efetch 16.2
##
## Format Selection
##
## -format Format of record or report
## -mode text, xml, asn.1, json
## -style master, conwithfeat
##
## Direct Record Selection
##
## -db Database name
## -id Unique identifier or accession number
## -input Read identifier(s) from file instead of stdin
##
## Sequence Range
##
## -seq_start First sequence position to retrieve
## -seq_stop Last sequence position to retrieve
## -strand 1 = forward DNA strand, 2 = reverse complement
## (otherwise strand minus is set if start > stop)
## -forward Force strand 1
## -revcomp Force strand 2
##
## Gene Range
##
## -chr_start Sequence range from 0-based coordinates
## -chr_stop in gene docsum GenomicInfoType object
##
## Sequence Flags
##
## -complexity 0 = default, 1 = bioseq, 3 = nuc-prot set
## -extend Extend sequence retrieval in both directions
## -extrafeat Bit flag specifying extra features
## -showgaps Propagate component gaps
##
## Subset Retrieval
##
## -start First record to fetch
## -stop Last record to fetch
##
## Miscellaneous
##
## -raw Skip database-specific XML modifications
## -express Direct sequence retrieval in groups of 5
## -immediate Express mode on a single record at a time
##
## Format Examples
##
## -db -format -mode Report Type
## ___ _______ _____ ___________
##
## (all)
## docsum DocumentSummarySet XML
## docsum json DocumentSummarySet JSON
## full Same as native except for mesh
## uid Unique Identifier List
## url Entrez URL
## xml Same as -format full -mode xml
##
## bioproject
## native BioProject Report
## native xml RecordSet XML
##
## biosample
## native BioSample Report
## native xml BioSampleSet XML
##
## biosystems
## native xml Sys-set XML
##
## clinvar
## variation Older Format
## variationid Transition Format
## vcv VCV Report
## clinvarset RCV Report
##
## gds
## native xml RecordSet XML
## summary Summary
##
## gene
## full_report Detailed Report
## gene_table Gene Table
## native Gene Report
## native asn.1 Entrezgene ASN.1
## native xml Entrezgene-Set XML
## tabular Tabular Report
##
## homologene
## alignmentscores Alignment Scores
## fasta FASTA
## homologene Homologene Report
## native Homologene List
## native asn.1 HG-Entry ASN.1
## native xml Entrez-Homologene-Set XML
##
## mesh
## full Full Record
## native MeSH Report
## native xml RecordSet XML
##
## nlmcatalog
## native Full Record
## native xml NLMCatalogRecordSet XML
##
## pmc
## bioc PubTator Central BioC XML
## medline MEDLINE
## native xml pmc-articleset XML
##
## pubmed
## abstract Abstract
## bioc PubTator Central BioC XML
## medline MEDLINE
## native asn.1 Pubmed-entry ASN.1
## native xml PubmedArticleSet XML
##
## (sequences)
## acc Accession Number
## est EST Report
## fasta FASTA
## fasta xml TinySeq XML
## fasta_cds_aa FASTA of CDS Products
## fasta_cds_na FASTA of Coding Regions
## ft Feature Table
## gb GenBank Flatfile
## gb xml GBSet XML
## gbc xml INSDSet XML
## gene_fasta FASTA of Gene
## gp GenPept Flatfile
## gp xml GBSet XML
## gpc xml INSDSet XML
## gss GSS Report
## ipg Identical Protein Report
## ipg xml IPGReportSet XML
## native text Seq-entry ASN.1
## native xml Bioseq-set XML
## seqid Seq-id ASN.1
##
## snp
## json Reference SNP Report
##
## sra
## native xml EXPERIMENT_PACKAGE_SET XML
## runinfo xml SraRunInfo XML
##
## structure
## mmdb Ncbi-mime-asn1 strucseq ASN.1
## native MMDB Report
## native xml RecordSet XML
##
## taxonomy
## native Taxonomy List
## native xml TaxaSet XML
##
## Examples
##
## efetch -db pubmed -id 6271474,5685784,4882854,6243420 -format xml |
## xtract -pattern PubmedArticle -element MedlineCitation/PMID "#Author" \
## -block Author -position first -sep " " -element Initials,LastName \
## -block Article -element ArticleTitle
##
## efetch -db nuccore -id CM000177.6 -format gb -style conwithfeat -showgaps
##
## efetch -db nuccore -id 1121073309 -format gbc -style master
##
## efetch -db nuccore -id JABRPF010000000 -format gb
##
## efetch -db nuccore -id JABRPF010000001 -format gb
##
## efetch -db protein -id 3OQZ_a -format fasta
##
## esearch -db protein -query "conotoxin AND mat_peptide [FKEY]" |
## efetch -format gpc |
## xtract -insd complete mat_peptide "%peptide" product mol_wt peptide |
## grep -i conotoxin | sort -t $'\t' -u -k 2,2n | head -n 8
##
## esearch -db gene -query "DDT [GENE] AND mouse [ORGN]" |
## efetch -format docsum |
## xtract -pattern GenomicInfoType -element ChrAccVer ChrStart ChrStop |
## xargs -n 3 sh -c 'efetch -db nuccore -format gb \
## -id "$0" -chr_start "$1" -chr_stop "$2"'
Again, there are a few important parameters to highlight here:
The -format parameter decides what format to retrieve the data. Each NCBI databse supports multiple formats so you need to specify which format you would like.
The -db parameter decided which NCBI database you will search for the associated metadata. The accession number you use must be compatible with the chosen database. Here we are using SRA accession numbers so we must specify the SRA database.
The -id parameter is the unique identifier or accession number you are using as a query. This accession number must be in the same format as the database you are searching. Again, since we are searching the SRA database, we need to use an SRA accession number.
If you look back at the SRA webpage for the SRR4413906 run, you will see an SRA Study field near the bottom. This accession number (SRP091443) can be used to find all of the sequencing libraries associated with that given study.
Fetch run information for all runs in a given study:
efetch -format runinfo -db sra -id SRP091443 > tutorial/runinfo.csv
Display the contents of the run information file:
cat tutorial/runinfo.csv
## Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash
## SRR4413836,2017-03-13 16:26:12,2016-10-11 12:04:14,10453611,784315801,10453611,75,312,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413836.sralite.1,SRX2236907,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738020,SAMN05894757,simple,10090,Mus musculus,GSM2341284,,,,,,,no,,,,,GEO,SRA483374,,public,7C407137062FCA75F46916F7D6801218,6058D500A9A62F05BCF6D0D58891064D
## SRR4413837,2017-03-13 16:26:12,2016-10-11 12:04:57,12829832,962659197,12829832,75,396,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413837.sralite.1,SRX2236907,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738020,SAMN05894757,simple,10090,Mus musculus,GSM2341284,,,,,,,no,,,,,GEO,SRA483374,,public,E6DB950A86FE4DAD14C73E25888D131F,6734B4DC23B6634851E574012695E474
## SRR4413838,2017-03-13 16:26:12,2016-10-11 12:05:44,11966150,897716683,11966150,75,358,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413838.sralite.1,SRX2236908,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738021,SAMN05894767,simple,10090,Mus musculus,GSM2341285,,,,,,,no,,,,,GEO,SRA483374,,public,20C7BFC5266F062437BF64ACE3BF1165,DCC4DF84A8ABD91A4B0EF419BF2C7D0B
## SRR4413839,2017-03-13 16:26:12,2016-10-11 12:05:46,14752324,1106774587,14752324,75,457,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413839.sralite.1,SRX2236908,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738021,SAMN05894767,simple,10090,Mus musculus,GSM2341285,,,,,,,no,,,,,GEO,SRA483374,,public,F4B65AC04944019F49B6F0F9C69A9470,A0D476D8107F72D960DBC82F038BD8B3
## SRR4413840,2017-03-13 16:26:12,2016-10-11 12:04:02,10247757,768961951,10247757,75,306,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413840.sralite.1,SRX2236909,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738022,SAMN05894768,simple,10090,Mus musculus,GSM2341286,,,,,,,no,,,,,GEO,SRA483374,,public,D2EBD277377781915EA9ADCD2CAF0E4D,6C812C3EF5F35A9C6047656001A295A2
## SRR4413841,2017-03-13 16:26:12,2016-10-11 12:04:50,12572395,943426387,12572395,75,389,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3841/SRR4413841.sralite.1,SRX2236909,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738022,SAMN05894768,simple,10090,Mus musculus,GSM2341286,,,,,,,no,,,,,GEO,SRA483374,,public,A802BB340EDF5F3AA9FD51EC6268BE77,580EA08FA204C4904A1CF0BFB393CA77
## SRR4413842,2017-03-13 16:26:12,2016-10-11 12:09:59,10936374,820558359,10936374,75,323,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413842.sralite.1,SRX2236910,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738023,SAMN05894760,simple,10090,Mus musculus,GSM2341287,,,,,,,no,,,,,GEO,SRA483374,,public,B821A81A218F7B566B0636EC7A579CA5,8735995D9426B6259E77DBF61E9F7AFC
## SRR4413843,2017-03-13 16:26:12,2016-10-11 12:05:09,13541604,1016078140,13541604,75,415,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413843.sralite.1,SRX2236910,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738023,SAMN05894760,simple,10090,Mus musculus,GSM2341287,,,,,,,no,,,,,GEO,SRA483374,,public,D4AE30A11A96D5E4394CBC07FD352153,895B6421372CB3763C8C4927F408C886
## SRR4413844,2017-03-13 16:26:12,2016-10-11 12:04:30,12101772,907866428,12101772,75,358,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413844.sralite.1,SRX2236911,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738024,SAMN05894759,simple,10090,Mus musculus,GSM2341288,,,,,,,no,,,,,GEO,SRA483374,,public,6DC02BD4D88806747B17ADD4565F0D0F,5FC07FCDB4437A4FDF7A6648C2BB93CF
## SRR4413845,2017-03-13 16:26:12,2016-10-11 12:04:44,14871363,1115688067,14871363,75,457,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3845/SRR4413845.sralite.1,SRX2236911,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738024,SAMN05894759,simple,10090,Mus musculus,GSM2341288,,,,,,,no,,,,,GEO,SRA483374,,public,EC569116668D2CD9878C2F7FFF131CDE,EE1581748314196F4707FC58003D700C
## SRR4413846,2017-03-13 16:26:12,2016-10-11 12:03:44,8727101,654719767,8727101,75,260,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413846.sralite.1,SRX2236912,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738025,SAMN05894758,simple,10090,Mus musculus,GSM2341289,,,,,,,no,,,,,GEO,SRA483374,,public,4B03AB7DB80F430654BC723C5798B5B7,E7AAF6D8BFBF1E3D2A0B61C8E7FC57BC
## SRR4413847,2017-03-13 16:26:12,2016-10-11 12:04:24,10786677,809266394,10786677,75,334,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413847.sralite.1,SRX2236912,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738025,SAMN05894758,simple,10090,Mus musculus,GSM2341289,,,,,,,no,,,,,GEO,SRA483374,,public,CA01CCB01A7DCA09CC572C4953AF29BF,525C790EAF6AADEF7D4B4BB6139C9CC7
## SRR4413848,2017-03-13 16:26:12,2016-10-11 12:05:45,12655644,949534177,12655644,75,381,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413848.sralite.1,SRX2236913,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738026,SAMN05894756,simple,10090,Mus musculus,GSM2341290,,,,,,,no,,,,,GEO,SRA483374,,public,7C93401222853CF39EC107C2316DAA3B,91FC15694C48A40BF127779C050844EB
## SRR4413849,2017-03-13 16:26:12,2016-10-11 12:06:13,15302722,1148192105,15302722,75,476,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413849.sralite.1,SRX2236913,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738026,SAMN05894756,simple,10090,Mus musculus,GSM2341290,,,,,,,no,,,,,GEO,SRA483374,,public,E0BF5946244178DE4AD10A474D8D9C6C,C8E063FAE967AFDE02728B32F19EC487
## SRR4413850,2017-03-13 16:26:12,2016-10-11 12:03:51,9791702,734673728,9791702,75,296,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413850.sralite.1,SRX2236914,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738027,SAMN05894755,simple,10090,Mus musculus,GSM2341291,,,,,,,no,,,,,GEO,SRA483374,,public,AC08DCB5C15BA49C40CF1B9EB0266B8C,827637E98B668A0B6C301007F5BC1409
## SRR4413851,2017-03-13 16:26:12,2016-10-11 12:04:31,11804657,885748535,11804657,75,369,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3851/SRR4413851.sralite.1,SRX2236914,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738027,SAMN05894755,simple,10090,Mus musculus,GSM2341291,,,,,,,no,,,,,GEO,SRA483374,,public,B360E76BED622A49147EDD118BC69502,921C610BCE99E69E7529E2C11763B2BC
## SRR4413852,2017-03-13 16:26:12,2016-10-11 12:04:12,10517837,789024963,10517837,75,314,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413852.sralite.1,SRX2236915,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738028,SAMN05894754,simple,10090,Mus musculus,GSM2341292,,,,,,,no,,,,,GEO,SRA483374,,public,606B83AF50D3BFEBA22CC7F385EE8246,ADC86570A4C13CED27952D35CF058ABE
## SRR4413853,2017-03-13 16:26:12,2016-10-11 12:04:55,12807335,960824201,12807335,75,396,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3853/SRR4413853.sralite.1,SRX2236915,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738028,SAMN05894754,simple,10090,Mus musculus,GSM2341292,,,,,,,no,,,,,GEO,SRA483374,,public,AC587EE00F6C90DA17BAA92BDFCCFEC8,4DDC433FC86F8FCB6DCB7C0A3AD9BDDB
## SRR4413854,2017-03-13 16:26:12,2016-10-11 12:03:37,8432141,632561001,8432141,75,252,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413854.sralite.1,SRX2236916,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738029,SAMN05894753,simple,10090,Mus musculus,GSM2341293,,,,,,,no,,,,,GEO,SRA483374,,public,F349A1FA3F6F26B1B3D5E8AB7C7F18EE,4C5A1CAB7FBA5F288F019B9158B6B286
## SRR4413855,2017-03-13 16:26:12,2016-10-11 12:04:08,10353231,776694263,10353231,75,321,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413855.sralite.1,SRX2236916,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738029,SAMN05894753,simple,10090,Mus musculus,GSM2341293,,,,,,,no,,,,,GEO,SRA483374,,public,A9E967CA4BA8C099609B8C3CE1740529,B403FAA2140B4BEE8771C292FE376964
## SRR4413856,2017-03-13 16:26:12,2016-10-11 12:04:30,11349739,851623523,11349739,75,341,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413856.sralite.1,SRX2236917,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738030,SAMN05894752,simple,10090,Mus musculus,GSM2341294,,,,,,,no,,,,,GEO,SRA483374,,public,86E01E20EFF10D90FC590AD512E6BBAB,AECAC51D36EC56865951282209446E1C
## SRR4413857,2017-03-13 16:26:12,2016-10-11 12:05:52,13779128,1033946800,13779128,75,429,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413857.sralite.1,SRX2236917,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738030,SAMN05894752,simple,10090,Mus musculus,GSM2341294,,,,,,,no,,,,,GEO,SRA483374,,public,7AF8DF6408B1CB065853BE8027513AFE,E59E32746E0A49E7EA0E7C9AA97D875F
## SRR4413858,2017-03-13 16:26:12,2016-10-11 12:04:47,10239543,768312336,10239543,75,308,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413858.sralite.1,SRX2236918,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738031,SAMN05894789,simple,10090,Mus musculus,GSM2341295,,,,,,,no,,,,,GEO,SRA483374,,public,CD5D3108CBCFF972CB4732CF7495D0FA,108AA073ABCD4824C3E77CA3C93F6FB9
## SRR4413859,2017-03-13 16:26:12,2016-10-11 12:05:45,12356513,927216282,12356513,75,385,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413859.sralite.1,SRX2236918,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738031,SAMN05894789,simple,10090,Mus musculus,GSM2341295,,,,,,,no,,,,,GEO,SRA483374,,public,0BFE9A4A4C7964F714196BF66BF65802,B480C02A0CCB8148522F1AD246108DBF
## SRR4413860,2017-03-13 16:26:12,2016-10-11 12:04:50,10732786,804531265,10732786,74,322,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413860.sralite.1,SRX2236919,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738032,SAMN05894788,simple,10090,Mus musculus,GSM2341296,,,,,,,no,,,,,GEO,SRA483374,,public,8A4460F2C19A749F577EB519A08EFDA8,BBD08892E0E20FC5EC4273D24BCE0D5D
## SRR4413861,2017-03-13 16:26:12,2016-10-11 12:05:45,13137657,984881985,13137657,74,407,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413861.sralite.1,SRX2236919,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738032,SAMN05894788,simple,10090,Mus musculus,GSM2341296,,,,,,,no,,,,,GEO,SRA483374,,public,E1606F7B10A480D7CF795B525F79DBA4,E7959D9775239BC14A516C26C09E4D68
## SRR4413862,2017-03-13 16:26:12,2016-10-11 12:04:59,10505117,787154275,10505117,74,315,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413862.sralite.1,SRX2236920,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738033,SAMN05894787,simple,10090,Mus musculus,GSM2341297,,,,,,,no,,,,,GEO,SRA483374,,public,BB723BDE1276E7311E939D2D76CE9693,B1524BF405DEBFEECD4CA70DEA13A758
## SRR4413863,2017-03-13 16:26:12,2016-10-11 12:05:47,12878682,965120869,12878682,74,399,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413863.sralite.1,SRX2236920,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738033,SAMN05894787,simple,10090,Mus musculus,GSM2341297,,,,,,,no,,,,,GEO,SRA483374,,public,0175BB5F46685062AD9B19ADB4074A5E,3A9D6B706A0947CFAB3849DFDB712082
## SRR4413864,2017-03-13 16:26:12,2016-10-11 12:04:40,9381749,703453617,9381749,74,283,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3864/SRR4413864.sralite.1,SRX2236921,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738034,SAMN05894786,simple,10090,Mus musculus,GSM2341298,,,,,,,no,,,,,GEO,SRA483374,,public,7FC4A272734AF4BECD9144080541B504,534601AFE41F27A62F92F8F357BD224A
## SRR4413865,2017-03-13 16:26:12,2016-10-11 12:04:59,11276368,845595383,11276368,74,351,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413865.sralite.1,SRX2236921,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738034,SAMN05894786,simple,10090,Mus musculus,GSM2341298,,,,,,,no,,,,,GEO,SRA483374,,public,7370A3737F9EC3F57FCDEFF000DC073B,9465D083BEE0A3CC14315D01916CBCBA
## SRR4413866,2017-03-13 16:26:12,2016-10-11 12:04:44,10084058,755841207,10084058,74,306,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3866/SRR4413866.sralite.1,SRX2236922,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738035,SAMN05894785,simple,10090,Mus musculus,GSM2341299,,,,,,,no,,,,,GEO,SRA483374,,public,3B1C4EC768E44A56BE60401E9C2DE390,F0FD76E3126A4C03729628853022720F
## SRR4413867,2017-03-13 16:26:12,2016-10-11 12:11:46,12113918,908058586,12113918,74,379,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413867.sralite.1,SRX2236922,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738035,SAMN05894785,simple,10090,Mus musculus,GSM2341299,,,,,,,no,,,,,GEO,SRA483374,,public,9891DF48DA3A45C056F6D8301AEE26B2,B57013092D6365E8736082139602A12B
## SRR4413868,2017-03-13 16:26:12,2016-10-11 12:07:29,12205895,915453136,12205895,75,367,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3868/SRR4413868.sralite.1,SRX2236923,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738036,SAMN05894784,simple,10090,Mus musculus,GSM2341300,,,,,,,no,,,,,GEO,SRA483374,,public,9EB0D7283376A3B226CAF53DB60E1B96,B847A31996ECB4853556A4ADFEBAE91C
## SRR4413869,2017-03-13 16:26:12,2016-10-11 12:14:01,14883414,1116280658,14883414,75,462,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413869.sralite.1,SRX2236923,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738036,SAMN05894784,simple,10090,Mus musculus,GSM2341300,,,,,,,no,,,,,GEO,SRA483374,,public,25DC87E41436265214463C2AE5EFE6F1,05FEE5C9D54AC75ED9763FAFA65410BE
## SRR4413870,2017-03-13 16:26:12,2016-10-11 12:05:45,12007505,900813395,12007505,75,362,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413870.sralite.1,SRX2236924,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738037,SAMN05894783,simple,10090,Mus musculus,GSM2341301,,,,,,,no,,,,,GEO,SRA483374,,public,2D3A9F31EF6EF0A283FA153D21AF9CDE,9268D559159B437993EBD539A1C9CC2A
## SRR4413871,2017-03-13 16:26:12,2016-10-11 12:05:54,14572359,1093275492,14572359,75,454,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413871.sralite.1,SRX2236924,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738037,SAMN05894783,simple,10090,Mus musculus,GSM2341301,,,,,,,no,,,,,GEO,SRA483374,,public,F4035D4EDC2221E3A5727AEBCB20FD55,CC79D992863DFC0D18AB026414E0B44E
## SRR4413872,2017-03-13 16:26:12,2016-10-11 12:07:13,11454777,859721234,11454777,75,343,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413872.sralite.1,SRX2236925,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738038,SAMN05894782,simple,10090,Mus musculus,GSM2341302,,,,,,,no,,,,,GEO,SRA483374,,public,52905380D97DDF4610054F46837A02EC,B9A8EC05C40C15F4DC5408C9B1741A03
## SRR4413873,2017-03-13 16:26:12,2016-10-11 12:10:42,13871130,1041096843,13871130,75,430,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413873.sralite.1,SRX2236925,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738038,SAMN05894782,simple,10090,Mus musculus,GSM2341302,,,,,,,no,,,,,GEO,SRA483374,,public,EDFBE79085D774B9A2D456A4343F8469,3B1F0A61FE3508B567304395001BB1D9
## SRR4413874,2017-03-13 16:26:12,2016-10-11 12:04:51,9959294,747393864,9959294,75,298,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3874/SRR4413874.sralite.1,SRX2236926,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738040,SAMN05894781,simple,10090,Mus musculus,GSM2341303,,,,,,,no,,,,,GEO,SRA483374,,public,CF7EF5D4B4649823088D99B5D1044F1B,25BD67E62877A8665835425355E1A0A2
## SRR4413875,2017-03-13 16:26:12,2016-10-11 12:05:10,12224882,917427209,12224882,75,378,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413875.sralite.1,SRX2236926,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738040,SAMN05894781,simple,10090,Mus musculus,GSM2341303,,,,,,,no,,,,,GEO,SRA483374,,public,86BCB05C949B488BE18C6E85EE7BC05D,1E9C4B58324D1EF534B6010DFBA97969
## SRR4413876,2017-03-13 16:26:12,2016-10-11 12:10:13,9966107,746657752,9966107,74,297,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413876.sralite.1,SRX2236927,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738039,SAMN05894780,simple,10090,Mus musculus,GSM2341304,,,,,,,no,,,,,GEO,SRA483374,,public,B020721262E5B97F4C153102D99BE207,F5A6262B70682D299D06BBEDAAB67B03
## SRR4413877,2017-03-13 16:26:12,2016-10-11 12:05:56,12299977,921598607,12299977,74,379,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413877.sralite.1,SRX2236927,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738039,SAMN05894780,simple,10090,Mus musculus,GSM2341304,,,,,,,no,,,,,GEO,SRA483374,,public,5B232CFF3319D87A1E4AAA0ABC5A2CBC,6F8DBFAA81710811725E017B9F554036
## SRR4413878,2017-03-13 16:26:12,2016-10-11 12:05:43,10003562,750225523,10003562,74,297,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413878.sralite.1,SRX2236928,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738041,SAMN05894779,simple,10090,Mus musculus,GSM2341305,,,,,,,no,,,,,GEO,SRA483374,,public,AD9271DF071AE162BD838ADFCB42FA88,0ED9C7BB839117611F8D1D312D6BD9C2
## SRR4413879,2017-03-13 16:26:12,2016-10-11 12:05:44,12359677,926977134,12359677,75,380,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413879.sralite.1,SRX2236928,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738041,SAMN05894779,simple,10090,Mus musculus,GSM2341305,,,,,,,no,,,,,GEO,SRA483374,,public,790F611310A5B99F79F59BA6F9518438,A8D28BE07CB0608E8691EFCA56CC0297
## SRR4413880,2017-03-13 16:26:12,2016-10-11 12:04:53,10588358,793720369,10588358,74,315,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3880/SRR4413880.sralite.1,SRX2236929,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738042,SAMN05894778,simple,10090,Mus musculus,GSM2341306,,,,,,,no,,,,,GEO,SRA483374,,public,AED98B82ECE69AC41583CE355FA9224A,1E838DC90B1657BEFA3046962D3FD672
## SRR4413881,2017-03-13 16:26:12,2016-10-11 12:06:17,13080477,980610316,13080477,74,402,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413881.sralite.1,SRX2236929,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738042,SAMN05894778,simple,10090,Mus musculus,GSM2341306,,,,,,,no,,,,,GEO,SRA483374,,public,2B6A8F91FF74496451A35EAF290143B4,3CE8E08F67BFC1F11E1E68A6E44824C6
## SRR4413882,2017-03-13 16:26:12,2016-10-11 12:06:05,10559109,791539025,10559109,74,316,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413882.sralite.1,SRX2236930,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738044,SAMN05894777,simple,10090,Mus musculus,GSM2341307,,,,,,,no,,,,,GEO,SRA483374,,public,296A7D8833DF5B07864293A34333C177,D3A70A1F8C7A3A47EC594F86CE261E0B
## SRR4413883,2017-03-13 16:26:12,2016-10-11 12:06:46,12967195,972151983,12967195,74,402,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413883.sralite.1,SRX2236930,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738044,SAMN05894777,simple,10090,Mus musculus,GSM2341307,,,,,,,no,,,,,GEO,SRA483374,,public,3A955F566E2A35169749691D5A2AD59E,5DB58040704B6719DD15990FE63C126C
## SRR4413884,2017-03-13 16:26:12,2016-10-11 12:06:52,12614385,946051489,12614385,74,372,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413884.sralite.1,SRX2236931,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738045,SAMN05894776,simple,10090,Mus musculus,GSM2341308,,,,,,,no,,,,,GEO,SRA483374,,public,95739DF9E5AB5F6E6591D347AAC9F685,519B3DFF5A8258E6DA7B85AF2D30C9F4
## SRR4413885,2017-03-13 16:26:13,2016-10-11 12:08:19,15716600,1178747269,15716600,75,481,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413885.sralite.1,SRX2236931,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738045,SAMN05894776,simple,10090,Mus musculus,GSM2341308,,,,,,,no,,,,,GEO,SRA483374,,public,B752ADF9EB9A54750C3A5940CFBB17E8,B43DE43C0E2E041B1D4D44202C9952E1
## SRR4413886,2017-03-13 16:26:13,2016-10-11 12:05:45,8779904,658636900,8779904,75,265,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413886.sralite.1,SRX2236932,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738043,SAMN05894775,simple,10090,Mus musculus,GSM2341309,,,,,,,no,,,,,GEO,SRA483374,,public,BB10DB5775C5237E05EDAD9C31F75BA2,5CCD06E1D83EA548AAF8CEBD8DBDFD46
## SRR4413887,2017-03-13 16:26:13,2016-10-11 12:06:22,10746226,806161521,10746226,75,335,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413887.sralite.1,SRX2236932,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738043,SAMN05894775,simple,10090,Mus musculus,GSM2341309,,,,,,,no,,,,,GEO,SRA483374,,public,EBCC7DBE946E4B58BE244E2F42FDAF68,AC484167DB7A8E9FEE940D9001173065
## SRR4413888,2017-03-13 16:26:13,2016-10-11 12:06:46,8311946,623504261,8311946,75,250,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413888.sralite.1,SRX2236933,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738046,SAMN05894774,simple,10090,Mus musculus,GSM2341310,,,,,,,no,,,,,GEO,SRA483374,,public,690806DC9A5510BE628137EDEE5FAC1D,BD1DEE51D901BD6AF828A41031603C04
## SRR4413889,2017-03-13 16:26:13,2016-10-11 12:06:05,10194817,764807993,10194817,75,317,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413889.sralite.1,SRX2236933,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738046,SAMN05894774,simple,10090,Mus musculus,GSM2341310,,,,,,,no,,,,,GEO,SRA483374,,public,9BE1320A4596959FC52F1D9BD42A1E58,91D5D96B5876CF7238017CC05FA0A3F1
## SRR4413890,2017-03-13 16:26:13,2016-10-11 12:06:03,8961079,672237633,8961079,75,272,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413890.sralite.1,SRX2236934,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738047,SAMN05894773,simple,10090,Mus musculus,GSM2341311,,,,,,,no,,,,,GEO,SRA483374,,public,384983C8233395954EE48E826EA97B62,5FB3961D3E4C22F879FEF1814163734B
## SRR4413891,2017-03-13 16:26:13,2016-10-11 12:06:12,10772877,808182638,10772877,75,337,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413891.sralite.1,SRX2236934,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738047,SAMN05894773,simple,10090,Mus musculus,GSM2341311,,,,,,,no,,,,,GEO,SRA483374,,public,FE35F5C062EB2E5735B1194BDB283800,9DA53200E69E1635910FA8E1DE9EB8BB
## SRR4413892,2017-03-13 16:26:13,2016-10-11 12:05:49,9051074,679023968,9051074,75,273,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413892.sralite.1,SRX2236935,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738048,SAMN05894772,simple,10090,Mus musculus,GSM2341312,,,,,,,no,,,,,GEO,SRA483374,,public,34B1D6666F70D770F167D8ADB5520A56,B81111DA70E08A9448FBB3A3D5B64F88
## SRR4413893,2017-03-13 16:26:13,2016-10-11 12:10:06,11057025,829565407,11057025,75,345,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413893.sralite.1,SRX2236935,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738048,SAMN05894772,simple,10090,Mus musculus,GSM2341312,,,,,,,no,,,,,GEO,SRA483374,,public,A9755F7FB817A150826D04111B23333F,47623713DF06C7A13DFE25E16EF39623
## SRR4413894,2017-03-13 16:26:13,2016-10-11 12:10:13,9038668,678558678,9038668,75,272,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413894.sralite.1,SRX2236936,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738049,SAMN05894771,simple,10090,Mus musculus,GSM2341313,,,,,,,no,,,,,GEO,SRA483374,,public,E73039B4A8F4445AD926F9463A2FA9BE,87885658724770434E58F55E02B359E5
## SRR4413895,2017-03-13 16:26:13,2016-10-11 12:06:24,11026745,827838504,11026745,75,343,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413895.sralite.1,SRX2236936,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738049,SAMN05894771,simple,10090,Mus musculus,GSM2341313,,,,,,,no,,,,,GEO,SRA483374,,public,44F38143238CDFD4483F0B1A272E71B8,E082539DAFC2D3794A6575C456288DEE
## SRR4413896,2017-03-13 16:26:13,2016-10-11 12:07:13,11027843,828254467,11027843,75,336,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413896.sralite.1,SRX2236937,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738050,SAMN05894770,simple,10090,Mus musculus,GSM2341314,,,,,,,no,,,,,GEO,SRA483374,,public,3191921210B6E61A1C06A9CD5AF78EB5,3B92F3C8557251682630E62C76A72F36
## SRR4413897,2017-03-13 16:26:13,2016-10-11 12:07:56,13329955,1001185683,13329955,75,418,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3897/SRR4413897.sralite.1,SRX2236937,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738050,SAMN05894770,simple,10090,Mus musculus,GSM2341314,,,,,,,no,,,,,GEO,SRA483374,,public,AD05028CFB0D71BEE15FB1EE3FC00642,BC554F796FF01A0885126BA6CF1E2BEC
## SRR4413898,2017-03-13 16:26:13,2016-10-11 12:06:58,9926540,744879452,9926540,75,296,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413898.sralite.1,SRX2236938,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738051,SAMN05894769,simple,10090,Mus musculus,GSM2341315,,,,,,,no,,,,,GEO,SRA483374,,public,1EA4F3C6ABA0D301E25D24CF3AB7B2EB,AAAAAED62FFAE7AB090ECB0DB6889AFA
## SRR4413899,2017-03-13 16:26:13,2016-10-11 12:07:10,12201059,915574301,12201059,75,377,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413899.sralite.1,SRX2236938,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738051,SAMN05894769,simple,10090,Mus musculus,GSM2341315,,,,,,,no,,,,,GEO,SRA483374,,public,FD4AC60ABD9264BB6CE0E54525FA2BF6,C4615B1A52AB49CA357E3802E6B666BA
## SRR4413900,2017-03-13 16:26:13,2016-10-11 12:06:46,9404245,705804022,9404245,75,283,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413900.sralite.1,SRX2236939,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738053,SAMN05894766,simple,10090,Mus musculus,GSM2341316,,,,,,,no,,,,,GEO,SRA483374,,public,1D5B4D5E4CB00AE0E72191912AFC5824,6E9750EE11751CA1BC76BC7DE3F233B5
## SRR4413901,2017-03-13 16:26:13,2016-10-11 12:07:27,11474818,861229384,11474818,75,357,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3901/SRR4413901.sralite.1,SRX2236939,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738053,SAMN05894766,simple,10090,Mus musculus,GSM2341316,,,,,,,no,,,,,GEO,SRA483374,,public,B49BE017011113F1E415ABD1D4DDD63F,BDF1C756B75EB9E661D93D42634169D6
## SRR4413902,2017-03-13 16:26:13,2016-10-11 12:06:31,8612170,646758002,8612170,75,263,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413902.sralite.1,SRX2236940,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738052,SAMN05894765,simple,10090,Mus musculus,GSM2341317,,,,,,,no,,,,,GEO,SRA483374,,public,525B7AF7171793EFBAF50DD93A32209A,17A48866558667F33660A8091C23E67C
## SRR4413903,2017-03-13 16:26:13,2016-10-11 12:07:26,10362564,778209492,10362564,75,326,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413903.sralite.1,SRX2236940,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738052,SAMN05894765,simple,10090,Mus musculus,GSM2341317,,,,,,,no,,,,,GEO,SRA483374,,public,24602FC93D6E7CFDCF452B9F1AFB2C0E,2D46D476D84FAA4B633FA1A1A6EBC2FE
## SRR4413904,2017-03-13 16:26:13,2016-10-11 12:08:17,9708959,728672641,9708959,75,293,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413904.sralite.1,SRX2236941,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738055,SAMN05894764,simple,10090,Mus musculus,GSM2341318,,,,,,,no,,,,,GEO,SRA483374,,public,F8745F74C181D90429A38F7817D3E828,027FAE7CB559A960B34199628A0FB688
## SRR4413905,2017-03-13 16:26:13,2016-10-11 12:09:22,11828727,887853912,11828727,75,369,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR441/3905/SRR4413905.sralite.1,SRX2236941,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738055,SAMN05894764,simple,10090,Mus musculus,GSM2341318,,,,,,,no,,,,,GEO,SRA483374,,public,24D59F8BD924444C69724B4A405D7C8A,632024C8C2B4F53090CC8A8CF1BE21E9
## SRR4413906,2017-03-13 16:26:13,2016-10-11 12:07:14,7322468,549911382,7322468,75,222,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413906.sralite.1,SRX2236942,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738054,SAMN05894763,simple,10090,Mus musculus,GSM2341319,,,,,,,no,,,,,GEO,SRA483374,,public,CE7FD7C81DB8FED9C080B0A204A399A6,5D64E25CEDB15409B96F9E45350E5467
## SRR4413907,2017-03-13 16:26:13,2016-10-11 12:06:47,8829601,663093221,8829601,75,276,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413907.sralite.1,SRX2236942,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738054,SAMN05894763,simple,10090,Mus musculus,GSM2341319,,,,,,,no,,,,,GEO,SRA483374,,public,A3EF276B512C8E35093BA4133A2EAAD5,3363E7DF27F9B73E77B4BEC88C9C8099
## SRR4413908,2017-03-13 16:26:13,2016-10-11 12:07:50,8241390,619285594,8241390,75,250,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR004/413/SRR4413908.sralite.1,SRX2236943,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738056,SAMN05894762,simple,10090,Mus musculus,GSM2341320,,,,,,,no,,,,,GEO,SRA483374,,public,82A29A796213CC4760E6715F92228852,8ECD5BC841D603ED047025B1D781C8F3
## SRR4413909,2017-03-13 16:26:13,2016-10-11 12:08:15,10009739,752135532,10009739,75,313,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413909.sralite.1,SRX2236943,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738056,SAMN05894762,simple,10090,Mus musculus,GSM2341320,,,,,,,no,,,,,GEO,SRA483374,,public,3F4E255C3F148B0B9F8587A97D05C5BD,9F5B5D5C22175C3EC10D0588F025BE24
## SRR4413910,2017-03-13 16:26:13,2016-10-11 12:09:00,12434411,932948608,12434411,75,370,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413910.sralite.1,SRX2236944,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738057,SAMN05894761,simple,10090,Mus musculus,GSM2341321,,,,,,,no,,,,,GEO,SRA483374,,public,96D9C8C420411479FFA30348B0BD7AAA,7BC31F04BB67F91E342F4011C028FDE3
## SRR4413911,2017-03-13 16:26:13,2016-10-11 12:09:37,15393816,1154996857,15393816,75,474,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR004/413/SRR4413911.sralite.1,SRX2236944,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS1738057,SAMN05894761,simple,10090,Mus musculus,GSM2341321,,,,,,,no,,,,,GEO,SRA483374,,public,0AB4D3C2727E41F44FD7FA0E5D7F7868,A1E76D75584CEF3CEAA9E5D93D97537F
## SRR5312162,2017-03-13 16:26:13,2017-03-03 16:05:25,67051064,5030467734,67051064,75,1927,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312162.sralite.1,SRX2612038,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022636,SAMN06475095,simple,10090,Mus musculus,GSM2521508,,,,,,,no,,,,,GEO,SRA483374,,public,78BA1792D4C6D8794AF3943AB1EFFED3,3CBE1F93ED1B21117B514A88DE7C0F4D
## SRR5312163,2017-03-13 16:26:13,2017-03-03 15:56:23,41452608,3109924248,41452608,75,1200,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312163.sralite.1,SRX2612039,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022637,SAMN06475112,simple,10090,Mus musculus,GSM2521509,,,,,,,no,,,,,GEO,SRA483374,,public,1C531F963E48FFA47609DC03FF3168EB,A30E49913B19141A1DDD66E19BDC5ED1
## SRR5312164,2017-03-13 16:26:13,2017-03-03 15:53:09,40334588,3026244869,40334588,75,1189,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312164.sralite.1,SRX2612040,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022638,SAMN06475111,simple,10090,Mus musculus,GSM2521510,,,,,,,no,,,,,GEO,SRA483374,,public,75014A0ACA15E23B41B82470C58A6B74,BF50C3ACD7B4A95EAD20F0C079D3C888
## SRR5312165,2017-03-13 16:26:13,2017-03-03 15:56:47,44950455,3372385607,44950455,75,1309,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312165.sralite.1,SRX2612041,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022639,SAMN06475110,simple,10090,Mus musculus,GSM2521511,,,,,,,no,,,,,GEO,SRA483374,,public,D3CCE4AC5771773D463C520C171E6FE4,730772DB0CFBE137F6681B86A8690717
## SRR5312166,2017-03-13 16:26:13,2017-03-03 15:53:30,40858234,3065390049,40858234,75,1176,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312166.sralite.1,SRX2612042,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022640,SAMN06475109,simple,10090,Mus musculus,GSM2521512,,,,,,,no,,,,,GEO,SRA483374,,public,EF822220F66A80880D528AE20BC70698,1E3CE226BE21ABE59091E7B278EA2E20
## SRR5312167,2017-03-13 16:26:13,2017-03-03 15:53:59,38782648,2910013346,38782648,75,1161,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312167.sralite.1,SRX2612043,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022641,SAMN06475108,simple,10090,Mus musculus,GSM2521513,,,,,,,no,,,,,GEO,SRA483374,,public,FDC49DC9022B64175D464BD18ACEDA07,13478FCC923E0D4E4153A5C5A95205B6
## SRR5312168,2017-03-13 16:26:13,2017-03-03 15:38:38,9695587,727436597,9695587,75,291,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312168.sralite.1,SRX2612044,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022642,SAMN06475107,simple,10090,Mus musculus,GSM2521514,,,,,,,no,,,,,GEO,SRA483374,,public,82BB2AAD1D3D26B13E00133986574D07,56C1C33FDFC8E590086C13B8EC92E4C6
## SRR5312169,2017-03-13 16:26:13,2017-03-03 15:38:18,11696039,877552968,11696039,75,363,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312169.sralite.1,SRX2612044,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022642,SAMN06475107,simple,10090,Mus musculus,GSM2521514,,,,,,,no,,,,,GEO,SRA483374,,public,2B64503DDA82FC2F56528BD998F4242E,B8946E680A2FA5396CF5480ECB99DFC4
## SRR5312170,2017-03-13 16:26:13,2017-03-03 15:38:49,9978608,748685791,9978608,75,302,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312170.sralite.1,SRX2612045,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022643,SAMN06475106,simple,10090,Mus musculus,GSM2521515,,,,,,,no,,,,,GEO,SRA483374,,public,C464852A5CEC6829297D8B57F9A47AA7,0987816CE2573B020F3AB31103C36687
## SRR5312171,2017-03-13 16:26:13,2017-03-03 15:40:05,11915809,894064840,11915809,75,373,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312171.sralite.1,SRX2612045,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022643,SAMN06475106,simple,10090,Mus musculus,GSM2521515,,,,,,,no,,,,,GEO,SRA483374,,public,FB44103F981ABCC2FF8D44180CB2F15A,901F879085B33BED7597D41CCC8B28D9
## SRR5312172,2017-03-13 16:26:13,2017-03-03 15:40:09,10363907,777580044,10363907,75,310,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312172.sralite.1,SRX2612046,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022644,SAMN06475105,simple,10090,Mus musculus,GSM2521516,,,,,,,no,,,,,GEO,SRA483374,,public,AEFCEA27C2781E1D6D0995E1E1C35F0A,349D39F859D7D6BCDE9695603A307E74
## SRR5312173,2017-03-13 16:26:13,2017-03-03 15:38:37,12505618,938290857,12505618,75,388,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312173.sralite.1,SRX2612046,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022644,SAMN06475105,simple,10090,Mus musculus,GSM2521516,,,,,,,no,,,,,GEO,SRA483374,,public,B88A593848DEE9AD1754B599BD382226,35E88642D9F991423C28CD77DCF04FFD
## SRR5312174,2017-03-13 16:26:13,2017-03-03 15:39:53,11737644,880656082,11737644,75,354,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312174.sralite.1,SRX2612047,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022645,SAMN06475104,simple,10090,Mus musculus,GSM2521517,,,,,,,no,,,,,GEO,SRA483374,,public,C15B654C93BBB3C57896363F71B66575,A1DFAAB5B21A0509FFA0B684ED3A94A2
## SRR5312175,2017-03-13 16:26:13,2017-03-03 15:39:43,14118510,1059316666,14118510,75,441,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312175.sralite.1,SRX2612047,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022645,SAMN06475104,simple,10090,Mus musculus,GSM2521517,,,,,,,no,,,,,GEO,SRA483374,,public,58B4F6A1DBEA3E974FA8F598AD4842AE,D339B21BAB747392A35F760CB93EAB0B
## SRR5312176,2017-03-13 16:26:13,2017-03-03 15:40:52,13747724,1031679464,13747724,75,416,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312176.sralite.1,SRX2612037,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022635,SAMN06475103,simple,10090,Mus musculus,GSM2521518,,,,,,,no,,,,,GEO,SRA483374,,public,0ACD99DD70CBD623C83FDF76B31CFD15,119E9DFFDFFB4EC1B4CA7C18195501BB
## SRR5312177,2017-03-13 16:26:13,2017-03-03 15:41:02,16392023,1230162717,16392023,75,513,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312177.sralite.1,SRX2612037,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022635,SAMN06475103,simple,10090,Mus musculus,GSM2521518,,,,,,,no,,,,,GEO,SRA483374,,public,FED242D0FE6EA5C2B9D7ECDAED2DF264,8F1C8D4860C47005905222E7A7727FDF
## SRR5312178,2017-03-13 16:26:13,2017-03-03 15:39:35,10494589,787429894,10494589,75,315,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312178.sralite.1,SRX2612048,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022646,SAMN06475102,simple,10090,Mus musculus,GSM2521519,,,,,,,no,,,,,GEO,SRA483374,,public,DAB5E609E71E4F9AFA616B5735AE64E9,B3ECA788FB69BDBB6D068F04EBEAEB84
## SRR5312179,2017-03-13 16:26:13,2017-03-03 15:39:02,12666962,950450488,12666962,75,393,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312179.sralite.1,SRX2612048,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022646,SAMN06475102,simple,10090,Mus musculus,GSM2521519,,,,,,,no,,,,,GEO,SRA483374,,public,244A22E43B70C6B450D9997716837DAC,124B116CF1453604A67A789EBACB97EA
## SRR5312180,2017-03-13 16:26:13,2017-03-03 15:53:28,42968571,3223420642,42968571,75,1225,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312180.sralite.1,SRX2612049,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022647,SAMN06475101,simple,10090,Mus musculus,GSM2521520,,,,,,,no,,,,,GEO,SRA483374,,public,E4F8F60DE03194DA59E1AEB0D634E914,E1F004B5AFFF18C9712D85204AD73F25
## SRR5312181,2017-03-13 16:26:13,2017-03-03 15:56:41,50229719,3767981322,50229719,75,1438,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312181.sralite.1,SRX2612050,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022648,SAMN06475100,simple,10090,Mus musculus,GSM2521521,,,,,,,no,,,,,GEO,SRA483374,,public,D0B8557CAF706217BBF366D7EEF48879,DCAF59EED6C58F22711E4E12424C8A11
## SRR5312182,2017-03-13 16:26:13,2017-03-03 15:50:23,39319287,2950007522,39319287,75,1140,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312182.sralite.1,SRX2612051,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022649,SAMN06475099,simple,10090,Mus musculus,GSM2521522,,,,,,,no,,,,,GEO,SRA483374,,public,FC0D3571E1B9CC0A6425795938DA16A1,9BD9EB2F7C5F8F62293C3341F5FC2EEB
## SRR5312183,2017-03-13 16:26:13,2017-03-03 15:48:33,35821402,2687303534,35821402,75,1027,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312183.sralite.1,SRX2612052,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022650,SAMN06475098,simple,10090,Mus musculus,GSM2521523,,,,,,,no,,,,,GEO,SRA483374,,public,0EF97B891D04F69C3B2A36FE15ED5281,07CBAFBB7F50F4A3DA13A30A8A59A916
## SRR5312184,2017-03-13 16:26:13,2017-03-03 15:52:07,44930408,3370670751,44930408,75,1288,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312184.sralite.1,SRX2612053,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022651,SAMN06475097,simple,10090,Mus musculus,GSM2521524,,,,,,,no,,,,,GEO,SRA483374,,public,499FB4CDC506F7D6D73D58E89A584870,AE368D46A58E8E7E297CE2B8173E20CB
## SRR5312185,2017-03-13 16:26:13,2017-03-03 15:57:54,42204949,3166581377,42204949,75,1217,,https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/312/SRR5312185.sralite.1,SRX2612054,,ChIP-Seq,ChIP,GENOMIC,PAIRED,0,0,ILLUMINA,NextSeq 500,SRP091443,PRJNA347885,2,347885,SRS2022652,SAMN06475096,simple,10090,Mus musculus,GSM2521525,,,,,,,no,,,,,GEO,SRA483374,,public,06660C75A27CA7D6D7B5527EDAB18C3A,81CC086337BDFB826E66BD126D352B80
The run information file contains all of the metadata about each run in the given study. Some fields contain information on the sequencing itself (e.g., Number of reads, Average read length, and Library layout) and others contain information about the sample the run was prepared from (e.g. Sex, Disease, Tumor).
The exercises below are intended to test your knowledge of querying and downloading sequencing data. The solution to each exercise is blurred, only after attempting to solve the exercise yourself should you look at the solution. Should you need any help, please ask one of the instructors.
Create a directory to store the output files from each exercise:
mkdir exercises
mkdir exercises/ex1
mkdir exercises/ex2
mkdir exercises/ex3
Use the SRA website to search for an SRA study with accession number SRP094580. Once you have found the study, send all of the runs to the ‘Run Selector’. Then answer the following questions:
119
Mus musculus (mouse) and 129SV/Jae/C57BL6J
SRR5077666
efetch command to download and save the run information into a file called runinfo.csv in the exercises/ex1 directory:efetch -format runinfo -db sra -id SRP094580 > exercises/ex1/runinfo.csv
efetch command to download and save the run information from SRA study SRP000002 into a file called runinfo.csv in the exercises/ex2 directory:efetch -format runinfo -db sra -id SRP000002 > exercises/ex2/runinfo.csv
runids.txt in the exercises/ex2 directory with the SRR accession number of all the runs in the study. You can do this manually by looking at the file, or you can try to solve the problem using command line tools (e.g., sort, cut):cat exercises/ex2/runinfo.csv | # Print the contents of the file to the standard output
cut -d "," -f 1 | # Cut out the 1st field of each line, using "," as a field delimiter
tail -n +2 | # Print standard output beginning from line 2
> exercises/ex2/runids.txt # Redirect standard output to a file
prefetch command:prefetch --output-directory exercises/ex2 --option-file exercises/ex2/runids.txt
##
## 2022-09-23T16:31:48 prefetch.2.11.0: 1) Downloading 'SRR000066'...
## 2022-09-23T16:31:48 prefetch.2.11.0: Downloading via HTTPS...
## 2022-09-23T16:33:26 prefetch.2.11.0: HTTPS download succeed
## 2022-09-23T16:33:26 prefetch.2.11.0: 'SRR000066' is valid
## 2022-09-23T16:33:26 prefetch.2.11.0: 1) 'SRR000066' was downloaded successfully
##
## 2022-09-23T16:33:27 prefetch.2.11.0: 2) Downloading 'SRR000067'...
## 2022-09-23T16:33:27 prefetch.2.11.0: Downloading via HTTPS...
## 2022-09-23T16:34:42 prefetch.2.11.0: HTTPS download succeed
## 2022-09-23T16:34:42 prefetch.2.11.0: 'SRR000067' is valid
## 2022-09-23T16:34:42 prefetch.2.11.0: 2) 'SRR000067' was downloaded successfully
fastq-dump --maxSpotId 100 --outdir exercises/ex2/SRR000066 exercises/ex2/SRR000066/SRR000066.sra
fastq-dump --maxSpotId 100 --outdir exercises/ex2/SRR000067 exercises/ex2/SRR000067/SRR000067.sra
## Read 100 spots for exercises/ex2/SRR000066/SRR000066.sra
## Written 100 spots for exercises/ex2/SRR000066/SRR000066.sra
## Read 100 spots for exercises/ex2/SRR000067/SRR000067.sra
## Written 100 spots for exercises/ex2/SRR000067/SRR000067.sra
efetch command to download and save the run information from SRA study SRP000599 into a file called runinfo.csv in the exercises/ex3 directory:efetch -format runinfo -db sra -id SRP000599 > exercises/ex3/runinfo.csv
runids.txt in the exercises/ex3 directory with the SRR accession number of the run with the smallest number of reads. You can do this manually by looking at the file, or you can try to solve the problem using command line tools (e.g., sort, cut):cat exercises/ex3/runinfo.csv | # Print the contents of the file to the standard output
sort -t "," -k 4n | # Sort by the 4th field of each line numerically, using "," as a field delimiter
cut -d "," -f 1 | # Cut out the 1st field of each line, using "," as a field delimiter
tail -n +2 | # Print standard output beginning from line 2
head -n 1 | # Print the first line of the standard output
> exercises/ex3/runids.txt # Redirect standard output to a file
prefetch --output-directory exercises/ex3 --option-file exercises/ex3/runids.txt
##
## 2022-09-23T16:34:52 prefetch.2.11.0: 1) Downloading 'SRR013564'...
## 2022-09-23T16:34:52 prefetch.2.11.0: Downloading via HTTPS...
## 2022-09-23T16:34:57 prefetch.2.11.0: HTTPS download succeed
## 2022-09-23T16:34:57 prefetch.2.11.0: 'SRR013564' is valid
## 2022-09-23T16:34:57 prefetch.2.11.0: 1) 'SRR013564' was downloaded successfully
fastq-dump --minSpotId 100 --maxSpotId 500 --outdir exercises/ex3/SRR013564 exercises/ex3/SRR013564/SRR013564.sra
## Read 401 spots for exercises/ex3/SRR013564/SRR013564.sra
## Written 401 spots for exercises/ex3/SRR013564/SRR013564.sra